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Yorodumi- PDB-5oj7: Sirtuin 4 orthologue from Xenopus Tropicalis in complex with ADP-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oj7 | |||||||||
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Title | Sirtuin 4 orthologue from Xenopus Tropicalis in complex with ADP-ribose | |||||||||
Components | NAD-dependent protein deacylase | |||||||||
Keywords | HYDROLASE / Sirt4 Deacylase Posttranslational modification | |||||||||
Function / homology | Function and homology information NAD-dependent protein lysine deacetylase activity / protein deacetylation / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transferase activity / mitochondrial matrix / zinc ion binding Similarity search - Function | |||||||||
Biological species | Xenopus tropicalis (tropical clawed frog) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | |||||||||
Authors | Pannek, M. / Steegborn, C. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features. Authors: Pannek, M. / Simic, Z. / Fuszard, M. / Meleshin, M. / Rotili, D. / Mai, A. / Schutkowski, M. / Steegborn, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oj7.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oj7.ent.gz | 104.4 KB | Display | PDB format |
PDBx/mmJSON format | 5oj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/5oj7 ftp://data.pdbj.org/pub/pdb/validation_reports/oj/5oj7 | HTTPS FTP |
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-Related structure data
Related structure data | 5ojnC 5ojoC 4twiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32100.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog) Gene: sirt4, TGas015j14.1-001 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): CodonPlus References: UniProt: Q28CB4, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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-Non-polymers , 5 types, 268 molecules
#2: Chemical | ChemComp-AR6 / [( | ||||
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#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.6 % / Description: Diamond-shape |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M BICINE pH 8.0 17% PEG6000 / PH range: 7.8-8.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.911656 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 2, 2015 / Details: MIRROR |
Radiation | Monochromator: SI111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.911656 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→20 Å / Num. obs: 39280 / % possible obs: 99.8 % / Redundancy: 5.1 % / CC1/2: 1 / Rrim(I) all: 0.036 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.58→1.62 Å / Redundancy: 5.2 % / Num. unique obs: 2868 / CC1/2: 0.7 / Rrim(I) all: 0.853 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TWI Resolution: 1.58→19.73 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.184 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.097 Å2
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Refinement step | Cycle: 1 / Resolution: 1.58→19.73 Å
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Refine LS restraints |
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